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Sample GSM8514730 Query DataSets for GSM8514730
Status Public on Sep 17, 2024
Title NUC1-nuc2_P40_Rep4
Sample type SRA
 
Source name Leaf
Organism Zea mays
Characteristics tissue: Leaf
u. maydis_strain: NUC1-nuc2
fraction: P40
genotype: B73
Treatment protocol The Z. mays seedlings were infected with a suspension of U. maydis sporidia in sterile water using a syringe infection method.
Growth protocol Z. mays seedlings were grown under controlled temperature and humidity conditions throughout with a 16 h light and 8 h dark cycle. U. maydis sporidia were grown at 28ºC under constant shaking at 200 rpm till OD600 of the culture reached 0.8. At this stage the cells were harvested and used for infection.
Extracted molecule total RNA
Extraction protocol RNA was extracted from all the different samples using TRIzol method following the manufacturer’s protocol.
We used the commertial kit NEB Ultra II stranded
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Untrimmed reads were mapped to the Maize Genome v4 using Hisat2 with default parameters.
The resulting bam file was analyzed using Strigtie package and the gff3 file from AGP v4 version with default paramenters, resulting in a mapping gtf file for each sample.
Assembly: Zea_mays.AGPv4.dna.toplevel.fa
Supplementary files format and content: gtf files of mapping reads
 
Submission date Sep 13, 2024
Last update date Sep 17, 2024
Contact name Patricia Baldrich Gonzalez
E-mail(s) pbaldrich@ucdavis.edu
Organization name University of California - Davis
Department Genome Center
Lab Meyers Lab
Street address 451 Health Sciences Dr., Davis, CA 95616
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL34900
Series (1)
GSE277127 Evaluating the effect of secreted ribonucleases from Ustilago maydis on the extracellular RNA profile/repertoire of Zea mays during corn smut disease
Relations
BioSample SAMN43760909
SRA SRX26078388

Supplementary file Size Download File type/resource
GSM8514730_nuc1_nuc2_P40_Rep4_ZmaST.gtf.gz 9.6 Mb (ftp)(http) GTF
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Raw data are available in SRA

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